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SNV:21-29543953-C-T (GRCh38)

Dataset

gnomAD v3.1.2

	Genomes
Filters	Pass
Allele Count	98517
Allele Number	151900
Allele Frequency	0.6486
Grpmax Filtering AF (95% confidence)	0.7005 South Asian
Number of homozygotes	32565
Mean depth of coverage	31.9

External Resources

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Genetic Ancestry Group Frequencies

gnomAD
HGDP
1KG
Local Ancestry


	735	912	300	0.8059
	228	316	84	0.7215
	3474	4822	1266	0.7204
	47778	68004	16858	0.7026
	7357	10554	2561	0.6971
	3592	5156	1262	0.6967
	10465	15264	3568	0.6856
	2361	3472	791	0.6800
	1340	2084	434	0.6430
	21187	41316	5441	0.5128
XX	50234	77732	16593	0.6462
XY	48283	74168	15972	0.6510
Total	98517	151900	32565	0.6486

Include:ExomesGenomes


	220	308	80	0.7143
	317	456	107	0.6952
	48	70	17	0.6857
	203	298	71	0.6812
	226	332	77	0.6807
	39	96	11	0.4063
XX	386	568	136	0.6796
XY	667	992	227	0.6724
Total	1053	1560	363	0.6750

Related Variants

Other Alternate Alleles

This variant is multiallelic. Other alternate alleles are:

21-29543953-C-CTTTTTT

Nearby Variants

View variants located within 20 bases of this variant.

Variant Effect Predictor

This variant falls on 7 transcripts in 2 genes.

Note The gene symbols shown below are provided by VEP and may differ from the symbol shown on gene pages.

intron
1. GRIK1
  1. ENST00000327783.8
    Different version of MANE Select transcript for GRIK1
    HGVSc
    c.2608-6069G>A
  2. ENST00000389124.6
    HGVSc
    c.2608-6175G>A
  3. ENST00000389125.7
    HGVSc
    c.2563-6568G>A
2. BACH1
  1. ENST00000422809.5
    HGVSc
    c.473-38359C>T
  2. ENST00000468059.1
    HGVSc
    c.326-53617C>T

In Silico Predictors

Transcript-specific predictors SIFT and Polyphen are listed with Variant Effect Predictor annotations.

CADD: 0.739
SpliceAI: 0.00 (no_consequence)

Genomic Constraint of Surrounding 1kb Region

Genomic constraint values displayed are for the region: 21-29543000-29544000

Expected	Observed	Constraint
170.3	183	Z = -0.97 o/e = 1.07

Age Distribution

Exome
Genome

Variant carriers
All individuals

Include heterozygous variant carriersInclude homozygous variant carriersCompare to all individuals

Sequencing types:

Genotype Quality Metrics

Genotype quality
Depth
Allele balance for heterozygotes

Exome
Genome

Variant carriers
All individuals

Compare to all individualsSequencing types:

Site Quality Metrics

Metric distribution
All metric values

Exome
Genome

Metric: Sequencing types:

Value: 1.075e+8 (genome samples)

Site quality approximation for all variants with AF >= 0.5.

Metric	Genome samples
SiteQuality	1.075e+8
InbreedingCoeff	0.036
AS_FS	4.822e-16
AS_MQ	59.997
AS_MQRankSum	-0.018
AS_pab_max	1
AS_QUALapprox	1.075e+8
AS_QD	23.702
AS_ReadPosRankSum	0.29
AS_SOR	0.684
AS_VarDP	6.6566
AS_VQSLOD	20.272

Read Data

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